Input and runtime details for job 6756176 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 6756176 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:22:58 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:23:17 CET 2018
	CopraRNA Finished & Post-Processing		@ Fri Feb 16 20:01:55 CET 2018
	Post-Processing Finished		@ Fri Feb 16 20:02:03 CET 2018
	Job Completed		@ Fri Feb 16 20:02:30 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6756176&toolName=CopraRNA ( 30 days expiry )

Description of the job

DsrA

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation	Additional homologs
7	4.438e-05	0.02042	b0794	ybhF	-10.77	0.009494	150 -- 165	11 -- 26	putative ABC transporter ATPase		_____________149______________166\n_____________\|________________\|\n5'-UAC...UGAUG________________GCCAG...GUU-3'\n______________CGUUACGCCAGGGAAU\n______________\|\|\|\|\|\|:\|\|\|\|\|:\|\|\|\n______________GCAAUGUGGUCCUUUA\n3'-UUU...UUUAA________________GACUA...CAA-5'\n_____________\|________________\|\n_____________27_______________10\n	157 -- 163	13 -- 19	-25.1629 kcal/mol	6.0475 kcal/mol	8.34814 kcal/mol	149 166@LB@ \| \|@LB@5'-UAC...UGAUG GCCAG...GUU-3'@LB@ CGUUACGCCAGGGAAU@LB@ \|\|\|\|\|\|:\|\|\|\|\|:\|\|\|@LB@ GCAAUGUGGUCCUUUA@LB@3'-UUU...UUUAA GACUA...CAA-5'@LB@ \| \|@LB@ 27 10@LB@@LB@@LB@Energy -10.77 kcal/mol@LB@Hybridization Energy -25.1629 kcal/mol@LB@Unfolding Energy - mRNA 6.0475 kcal/mol@LB@Unfolding Energy - sRNA 8.34814 kcal/mol@LB@@LB@Position - mRNA 150 -- 165@LB@Position - sRNA 11 -- 26@LB@Position Seed - mRNA 157 -- 163@LB@Position Seed - sRNA 13 -- 19@LB@
19	0.0004926	0.08107	b0820	ybiT	-10.62	0.010514	37 -- 84	2 -- 44	ABC-F family putative regulatory ATPase		_____________36________________________________________________85\n_____________\|_________________________________________________\|\n5'-CCU...GUAUU________A___U_______A__CCA__U_A___U______A_______ACGAA...UUG-3'\n______________GGAAGCGC_UUA__AAGUUC_UU___GC_C_CAG_GAAAUC_GAUGUGU\n______________:\|\|\|\|\|:\|_\|\|\|__\|\|:\|\|\|_\|\|___:\|_\|_\|\|\|_\|\|\|\|\|\|_\|\|\|\|\|\|\|\n______________UCUUCGUG_AAU__UUUAAG_AA___UG_G_GUC_CUUUAG_CUACACA\n3'-UUU...UUCGU____________UU______C_______U____________A_______A-5'\n_____________\|_________________________________________________\|\n_____________45________________________________________________1\n	38 -- 44	37 -- 43	-34.6599 kcal/mol	11.843 kcal/mol	12.1934 kcal/mol	36 85@LB@ \| \|@LB@5'-CCU...GUAUU A U A CCA U A U A ACGAA...UUG-3'@LB@ GGAAGCGC UUA AAGUUC UU GC C CAG GAAAUC GAUGUGU@LB@ :\|\|\|\|\|:\| \|\|\| \|\|:\|\|\| \|\| :\| \| \|\|\| \|\|\|\|\|\| \|\|\|\|\|\|\|@LB@ UCUUCGUG AAU UUUAAG AA UG G GUC CUUUAG CUACACA@LB@3'-UUU...UUCGU UU C U A A-5'@LB@ \| \|@LB@ 45 1@LB@@LB@@LB@Energy -10.62 kcal/mol@LB@Hybridization Energy -34.6599 kcal/mol@LB@Unfolding Energy - mRNA 11.843 kcal/mol@LB@Unfolding Energy - sRNA 12.1934 kcal/mol@LB@@LB@Position - mRNA 37 -- 84@LB@Position - sRNA 2 -- 44@LB@Position Seed - mRNA 38 -- 44@LB@Position Seed - sRNA 37 -- 43@LB@
169	0.01902	0.3625	b0858	ybjO	-5.59	0.239654	140 -- 156	25 -- 43	DUF2593 family inner membrane protein		_____________139__________________157\n_____________\|____________________\|\n5'-AUG...UGGCU____A_______________CCAAC...UUA-3'\n______________GAAG_CACU___AAAAUUUG\n______________\|\|\|\|_\|\|\|\|___\|\|\|\|\|\|:\|\n______________CUUC_GUGA___UUUUAAGC\n3'-UUU...UCGUU_________AUU________AAUGU...CAA-5'\n_____________\|____________________\|\n_____________44___________________24\n	150 -- 156	25 -- 31	-11.6219 kcal/mol	2.26879 kcal/mol	3.76226 kcal/mol	139 157@LB@ \| \|@LB@5'-AUG...UGGCU A CCAAC...UUA-3'@LB@ GAAG CACU AAAAUUUG@LB@ \|\|\|\| \|\|\|\| \|\|\|\|\|\|:\|@LB@ CUUC GUGA UUUUAAGC@LB@3'-UUU...UCGUU AUU AAUGU...CAA-5'@LB@ \| \|@LB@ 44 24@LB@@LB@@LB@Energy -5.59 kcal/mol@LB@Hybridization Energy -11.6219 kcal/mol@LB@Unfolding Energy - mRNA 2.26879 kcal/mol@LB@Unfolding Energy - sRNA 3.76226 kcal/mol@LB@@LB@Position - mRNA 140 -- 156@LB@Position - sRNA 25 -- 43@LB@Position Seed - mRNA 150 -- 156@LB@Position Seed - sRNA 25 -- 31@LB@
170	0.01916	0.363	b1202	ycgV	-6.78	0.125661	82 -- 88	39 -- 45	putative adhesin	b2647	_____________81______89\n_____________\|_______\|\n5'-ACU...UCUCU_______UCAUC...UUG-3'\n______________GAGAAGC\n______________:\|\|\|\|\|\|\n______________UUCUUCG\n3'-UUU...AUUCG_______UGAAU...CAA-5'\n_____________\|_______\|\n_____________46______38\n	82 -- 88	39 -- 45	-7.60605 kcal/mol	0.31609 kcal/mol	0.514773 kcal/mol	81 89@LB@ \| \|@LB@5'-ACU...UCUCU UCAUC...UUG-3'@LB@ GAGAAGC@LB@ :\|\|\|\|\|\|@LB@ UUCUUCG@LB@3'-UUU...AUUCG UGAAU...CAA-5'@LB@ \| \|@LB@ 46 38@LB@@LB@@LB@Energy -6.78 kcal/mol@LB@Hybridization Energy -7.60605 kcal/mol@LB@Unfolding Energy - mRNA 0.31609 kcal/mol@LB@Unfolding Energy - sRNA 0.514773 kcal/mol@LB@@LB@Position - mRNA 82 -- 88@LB@Position - sRNA 39 -- 45@LB@Position Seed - mRNA 82 -- 88@LB@Position Seed - sRNA 39 -- 45@LB@
59	0.003153	0.1645	b1220	ychO	-8.71	0.038404	242 -- 262	37 -- 56	putative invasin		_____________241___________________263\n_____________\|_____________________\|\n5'-UCA...UUACU________U______C_____AGCUA...CAA-3'\n______________CUUGCUUG_AGCAGG_GGUAC\n______________\|\|\|\|\|\|\|:_\|\|\|\|:\|_:\|:\|\|\n______________GAACGAAU_UCGUUC_UCGUG\n3'-UUU...ACUUU_______________U_____AAUUU...CAA-5'\n_____________\|_____________________\|\n_____________57____________________36\n	242 -- 248	50 -- 56	-24.8668 kcal/mol	9.95535 kcal/mol	6.20049 kcal/mol	241 263@LB@ \| \|@LB@5'-UCA...UUACU U C AGCUA...CAA-3'@LB@ CUUGCUUG AGCAGG GGUAC@LB@ \|\|\|\|\|\|\|: \|\|\|\|:\| :\|:\|\|@LB@ GAACGAAU UCGUUC UCGUG@LB@3'-UUU...ACUUU U AAUUU...CAA-5'@LB@ \| \|@LB@ 57 36@LB@@LB@@LB@Energy -8.71 kcal/mol@LB@Hybridization Energy -24.8668 kcal/mol@LB@Unfolding Energy - mRNA 9.95535 kcal/mol@LB@Unfolding Energy - sRNA 6.20049 kcal/mol@LB@@LB@Position - mRNA 242 -- 262@LB@Position - sRNA 37 -- 56@LB@Position Seed - mRNA 242 -- 248@LB@Position Seed - sRNA 50 -- 56@LB@
192	0.02295	0.3851	b1282	yciH	-4.88	0.338940	8 -- 32	15 -- 33	initiation factor function partial mimic SUI1 family		_____________7_________________________33\n_____________\|_________________________\|\n____5'-UUCGGUC________AAACUG___________CAUUC...UGC-3'\n______________AGGAGUUC______GUUACGCCGGG\n______________\|::\|:\|\|\|______\|\|\|\|\|:\|\|:\|\|\n______________UUUUUAAG______CAAUGUGGUCC\n3'-UUU...UGAAU_________________________UUUAG...CAA-5'\n_____________\|_________________________\|\n_____________34________________________14\n	9 -- 15	26 -- 32	-19.9664 kcal/mol	6.44674 kcal/mol	8.63649 kcal/mol	7 33@LB@ \| \|@LB@ 5'-UUCGGUC AAACUG CAUUC...UGC-3'@LB@ AGGAGUUC GUUACGCCGGG@LB@ \|::\|:\|\|\| \|\|\|\|\|:\|\|:\|\|@LB@ UUUUUAAG CAAUGUGGUCC@LB@3'-UUU...UGAAU UUUAG...CAA-5'@LB@ \| \|@LB@ 34 14@LB@@LB@@LB@Energy -4.88 kcal/mol@LB@Hybridization Energy -19.9664 kcal/mol@LB@Unfolding Energy - mRNA 6.44674 kcal/mol@LB@Unfolding Energy - sRNA 8.63649 kcal/mol@LB@@LB@Position - mRNA 8 -- 32@LB@Position - sRNA 15 -- 33@LB@Position Seed - mRNA 9 -- 15@LB@Position Seed - sRNA 26 -- 32@LB@
94	0.006975	0.2379	b1284	yciT	-8.66	0.039674	34 -- 64	15 -- 42	global regulator of transcription; DeoR family		_____________33_______________________________65\n_____________\|________________________________\|\n5'-GCA...AUCUC___A________GCA___C_____________UUGCU...CCA-3'\n______________GAG_UACUUAAA___GAA_UC_UUGCGCCAGG\n______________:\|\|_:\|\|\|\|\|\|\|___:\|\|_\|\|_\|\|:\|:\|\|\|\|\|\n______________UUC_GUGAAUUU___UUU_AG_AAUGUGGUCC\n3'-UUU...CGUUC__________________A__C__________UUUAG...CAA-5'\n_____________\|________________________________\|\n_____________43_______________________________14\n	58 -- 64	15 -- 21	-23.4161 kcal/mol	5.55126 kcal/mol	9.20431 kcal/mol	33 65@LB@ \| \|@LB@5'-GCA...AUCUC A GCA C UUGCU...CCA-3'@LB@ GAG UACUUAAA GAA UC UUGCGCCAGG@LB@ :\|\| :\|\|\|\|\|\|\| :\|\| \|\| \|\|:\|:\|\|\|\|\|@LB@ UUC GUGAAUUU UUU AG AAUGUGGUCC@LB@3'-UUU...CGUUC A C UUUAG...CAA-5'@LB@ \| \|@LB@ 43 14@LB@@LB@@LB@Energy -8.66 kcal/mol@LB@Hybridization Energy -23.4161 kcal/mol@LB@Unfolding Energy - mRNA 5.55126 kcal/mol@LB@Unfolding Energy - sRNA 9.20431 kcal/mol@LB@@LB@Position - mRNA 34 -- 64@LB@Position - sRNA 15 -- 42@LB@Position Seed - mRNA 58 -- 64@LB@Position Seed - sRNA 15 -- 21@LB@
82	0.005534	0.2146	b1342	ydaN	-6.57	0.141434	180 -- 206	30 -- 54	putative Zn(II) transporter		_____________179_________________________207\n_____________\|___________________________\|\n5'-CGU...AAUAA___G____U_AU_________GU____GCGAU...AUG-3'\n______________UGC_UUGA_G__GGAGGCACU__GGAA\n______________\|\|\|_\|\|:\|_\|__:\|\|:\|\|\|\|\|__::\|\|\n______________ACG_AAUU_C__UCUUCGUGA__UUUU\n3'-UUU...UUUGA__________GU_________AU____UAAGC...CAA-5'\n_____________\|___________________________\|\n_____________55__________________________29\n	194 -- 200	36 -- 42	-19.056 kcal/mol	6.29262 kcal/mol	6.19579 kcal/mol	179 207@LB@ \| \|@LB@5'-CGU...AAUAA G U AU GU GCGAU...AUG-3'@LB@ UGC UUGA G GGAGGCACU GGAA@LB@ \|\|\| \|\|:\| \| :\|\|:\|\|\|\|\| ::\|\|@LB@ ACG AAUU C UCUUCGUGA UUUU@LB@3'-UUU...UUUGA GU AU UAAGC...CAA-5'@LB@ \| \|@LB@ 55 29@LB@@LB@@LB@Energy -6.57 kcal/mol@LB@Hybridization Energy -19.056 kcal/mol@LB@Unfolding Energy - mRNA 6.29262 kcal/mol@LB@Unfolding Energy - sRNA 6.19579 kcal/mol@LB@@LB@Position - mRNA 180 -- 206@LB@Position - sRNA 30 -- 54@LB@Position Seed - mRNA 194 -- 200@LB@Position Seed - sRNA 36 -- 42@LB@
88	0.006209	0.2266	b1643	ydhI	-11.55	0.005389	141 -- 153	28 -- 40	DUF1656 family putative inner membrane efflux pump associated protein		_____________140___________154\n_____________\|_____________\|\n5'-UUU...UUUUC_____________AUUUA...GAU-3'\n______________GCACUUAAAGAAU\n______________\|\|\|\|\|\|\|\|\|:\|\|\|\n______________CGUGAAUUUUUUA\n3'-UUU...UUCUU_____________AGCAA...CAA-5'\n_____________\|_____________\|\n_____________41____________27\n	144 -- 150	31 -- 37	-15.2864 kcal/mol	2.10141 kcal/mol	1.63611 kcal/mol	140 154@LB@ \| \|@LB@5'-UUU...UUUUC AUUUA...GAU-3'@LB@ GCACUUAAAGAAU@LB@ \|\|\|\|\|\|\|\|\|:\|\|\|@LB@ CGUGAAUUUUUUA@LB@3'-UUU...UUCUU AGCAA...CAA-5'@LB@ \| \|@LB@ 41 27@LB@@LB@@LB@Energy -11.55 kcal/mol@LB@Hybridization Energy -15.2864 kcal/mol@LB@Unfolding Energy - mRNA 2.10141 kcal/mol@LB@Unfolding Energy - sRNA 1.63611 kcal/mol@LB@@LB@Position - mRNA 141 -- 153@LB@Position - sRNA 28 -- 40@LB@Position Seed - mRNA 144 -- 150@LB@Position Seed - sRNA 31 -- 37@LB@
117	0.009786	0.2694	b1706	ydiU	-6.16	0.177349	6 -- 27	36 -- 55	UPF0061 family protein		_____________5______________________28\n_____________\|______________________\|\n______5'-UGCAA____AUCAUU____________GAUAC...AUA-3'\n______________UUGC______GCGGGAGGCAUU\n______________\|\|\|\|______\|\|::\|\|:\|\|\|:\|\n______________AACG______CGUUCUUCGUGA\n3'-UUU...CUUUG____AAUU______________AUUUU...CAA-5'\n_____________\|______________________\|\n_____________56_____________________35\n	21 -- 27	36 -- 42	-19.2761 kcal/mol	6.93839 kcal/mol	6.17795 kcal/mol	5 28@LB@ \| \|@LB@ 5'-UGCAA AUCAUU GAUAC...AUA-3'@LB@ UUGC GCGGGAGGCAUU@LB@ \|\|\|\| \|\|::\|\|:\|\|\|:\|@LB@ AACG CGUUCUUCGUGA@LB@3'-UUU...CUUUG AAUU AUUUU...CAA-5'@LB@ \| \|@LB@ 56 35@LB@@LB@@LB@Energy -6.16 kcal/mol@LB@Hybridization Energy -19.2761 kcal/mol@LB@Unfolding Energy - mRNA 6.93839 kcal/mol@LB@Unfolding Energy - sRNA 6.17795 kcal/mol@LB@@LB@Position - mRNA 6 -- 27@LB@Position - sRNA 36 -- 55@LB@Position Seed - mRNA 21 -- 27@LB@Position Seed - sRNA 36 -- 42@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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